Hello Stephen, You can go from NP_ numbers to NM_ numbers using the 'refLink' table, then you can get location information from the 'refGene' table. Both tables are available from our downloads server:
http://hgdownload.cse.ucsc.edu/downloads.html Look for the assembly you wish to use, and then click "Annotation database" and look for the refLink and refGene files. Alternatively, you can use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to get this information. Start from the refLink table: group: Genes and Gene Prediction tracks track: RefSeq Genes table: refLink then hit "filter: create". Paste your list of NP_ numbers in the protAcc field and hit submit. Now choose "output format: selected fields from primary and related tables" and hit "get output". On the next page, choose the refGene table from the Linked tables section and hit "allow selection from checked tables". Select the 'protAcc' field from the refLink section and the name, chrom strand, txStart, txEnd and any other fields you wish to retrieve from the refGene section. Hit "get output". You should get the list of NP_ numbers along with NM_ numbers and their positions. I hope this is helpful. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/22/08 9:33 PM, Stephen Lillioja wrote: > I have some NP_ accession numbers and I want to Identify gene locations. Is there a file to convert these to NM_ numbers to do this? > > Thanks, > > Stephen Lillioja > Professor Stephen Lillioja > Health and Behavioural Sciences > Graduate School of Medicine > phone: 61 2 4221 5055 > FAX: 61 2 4221 5850 > mobile: 0419 780 826 > email: [email protected]<mailto:[email protected]> > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
